rs12524865

Positions:

• chr6-133875536-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109982.1(TARID):​n.403+13068G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,974 control chromosomes in the GnomAD database, including 9,189 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (9189 hom., cov: 31)
• Consequence: TARID NR_109982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

TARID (HGNC:50506): (TCF21 antisense RNA inducing promoter demethylation)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TARID	NR_109982.1	n.403+13068G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TARID	ENST00000607033.5	n.379+13068G>T		intron_variant, non_coding_transcript_variant		1
TARID	ENST00000606544.5	n.379+13068G>T		intron_variant, non_coding_transcript_variant		5
TARID	ENST00000607573.5	n.250+16151G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51313 AN: 151856 Hom.: 9173 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.355

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.338 AC: 51368 AN: 151974 Hom.: 9189 Cov.: 31 AF XY: 0.341 AC XY: 25332 AN XY: 74292

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.359

Alfa AF: 0.294 Hom.: 13134

Bravo AF: 0.359

Asia WGS AF: 0.448 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12524865; hg19: chr6-134196674;